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Fischer was born in Karlsruhe, Grand Duchy of Baden, in 1874. Studies medicine, folkloristics and history from 1893–1898 in Berlin, Freiburg and Munich. Promotion to Dr. med in 1898 and in 1900 habilitation for anatomy and anthropology at the University of Freiburg.[1] He became Director of the Anatomical Institute in Freiburg in 1918,[2] part of the University of Freiburg.[3]

In 1908 Fischer conducted field research in German Southwest Africa (now Namibia). He studied the Basters, offspring of German or Boer men who had fathered children by the native women (Hottentots) in that area. His study concluded with a call to prevent a "mixed race" by the prohibition of "mixed marriage" such as those he had studied. It included unethical medical practices on the Herero and Namaqua people.[8] He argued that while the existing Mischling descendants of the mixed marriages might be useful for Germany, he recommended that they should not continue to reproduce. His recommendations were followed and by 1912 interracial marriage was prohibited throughout the German colonies.[9][10] As a precursor to his experiments on Jews in Nazi Germany, he collected bones and skulls for his studies, in part from medical experimentation on African prisoners of war in Namibia during the Herero and Namaqua Genocide.[11][12]

His ideas expressed in this work, related to maintaining the purity of races, influenced future German legislation on race, including the Nuremberg laws.[10]

In the years of 1937–1938 Fischer and his colleagues analysed 600 children in Nazi Germany descending from French-African soldiers who occupied western areas of Germany after First World War; all children were illegally subjected to sterilization afterwards.[13]

Fischer didn't officially join the Nazi Party until 1940.[14] However, he was influential with National Socialists early on. A two-volume work, Foundations of Human Hereditary Teaching and Racial Hygiene published 1921 and 1932, and in 1936 published under Human Heredity Theory and Racial Hygiene, co-written by Erwin Baur and Fritz Lenz. The book served as the scientific basis for the Nazi's eugenic policies.[15] He also authored The Rehoboth Bastards and the Problem of Miscegenation among Humans (1913) (German: Die Rehobother Bastards und das Bastardierungsproblem beim Menschen), a field study which provided context for later racial debates, influenced German colonial legislation and provided scientific support for the Nuremberg laws.[16]

Under the Nazi regime, Fischer developed the physiological specifications used to determine racial origins and developed the so-called Fischer–Saller scale. He and his team experimented on Gypsies and African-Germans, taking blood and measuring skulls to find scientific validation for his theories.

Efforts to return the Namibian skulls harvested by Fischer were started with an investigation by the University of Freiburg in 2011 and completed with the return of the skulls in March 2014.[17][18][19]